Variant report

Variant	rs363100
Chromosome Location	chr4:3160307-3160308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3112733..3115394-chr4:3157286..3160905,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10006373	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10034669	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10488840	1.00[EUR][1000 genomes]
rs16844026	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16844028	1.00[EUR][1000 genomes]
rs2003530	0.97[EUR][1000 genomes]
rs2005787	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436280	0.92[EUR][1000 genomes]
rs28507598	0.83[EUR][1000 genomes]
rs28643391	0.99[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs3025825	0.99[EUR][1000 genomes]
rs362269	0.82[EUR][1000 genomes]
rs362274	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs362276	0.91[EUR][1000 genomes]
rs362278	1.00[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs362305	0.80[EUR][1000 genomes]
rs362310	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs362323	0.99[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs362338	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs363067	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363082	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363090	0.93[EUR][1000 genomes]
rs363091	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs363093	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.97[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs363097	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363098	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.95[EUR][1000 genomes]
rs363106	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs363124	0.93[EUR][1000 genomes]
rs363125	0.93[EUR][1000 genomes]
rs363128	1.00[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59147561	1.00[ASN][1000 genomes]
rs59588638	0.85[EUR][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6446724	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446725	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828882	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829069	1.00[CHD][hapmap]
rs6834455	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835567	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.93[EUR][1000 genomes]
rs6839274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7438553	0.96[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7665816	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667354	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	1.00[EUR][1000 genomes]
rs7688390	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993542	1.00[CHD][hapmap]
rs9993781	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs363100	OTOP1	cis	cerebellum	SCAN
rs363100	TMEM129	cis	parietal	SCAN
rs363100	SH3BP2	cis	cerebellum	SCAN
rs363100	JAKMIP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:3108600-3163000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:3108800-3164600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
8	chr4:3114800-3162800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:3115800-3161600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:3115800-3162800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:3125200-3163000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:3125200-3163200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:3126800-3164400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:3127000-3164400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:3127200-3163400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:3127200-3163400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:3127200-3163400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr4:3127200-3163600	Strong transcription	Fetal Intestine Large	intestine
19	chr4:3127200-3164200	Strong transcription	Fetal Muscle Leg	muscle
20	chr4:3127200-3164400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:3131200-3162600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:3134800-3162000	Weak transcription	Hela-S3	cervix
23	chr4:3137800-3163400	Strong transcription	Liver	Liver
24	chr4:3139600-3164800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr4:3144200-3161800	Strong transcription	GM12878-XiMat	blood
26	chr4:3145600-3164600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:3145800-3164000	Strong transcription	Adipose Nuclei	Adipose
28	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr4:3146000-3163400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:3146000-3163600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:3146200-3162600	Strong transcription	Brain Hippocampus Middle	brain
32	chr4:3146200-3163400	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:3146200-3164400	Strong transcription	Fetal Thymus	thymus
34	chr4:3146400-3162200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:3146400-3162400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:3146400-3163400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:3146400-3163400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:3146400-3163600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:3146400-3163800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:3146400-3164400	Strong transcription	Primary T cells from cord blood	blood
41	chr4:3146400-3164800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:3146600-3163600	Strong transcription	Placenta	Placenta
43	chr4:3146600-3164000	Strong transcription	Primary B cells from cord blood	blood
44	chr4:3146600-3164200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:3146600-3164800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:3147000-3164400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:3147200-3164000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:3147800-3164600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:3148000-3162200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:3148000-3163000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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